Metagenoms - Revision history

Dpuiu: /* Web sites */

2008-06-09T19:04:46Z

Web sites

← Older revision		Revision as of 19:04, 9 June 2008
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	* [http://www.hgsc.bcm.tmc.edu/microbiome-index.xsp Baylor HMP] list of 353 genomes targeted for sequencing by the 4 centers		* [http://www.hgsc.bcm.tmc.edu/microbiome-index.xsp Baylor HMP] list of 353 genomes targeted for sequencing by the 4 centers
	* [http://www.jcvi.org/cms/research/projects/hmp/overview/ JCVI HMP] 50 genomes (oral,skin,vagina)		* [http://www.jcvi.org/cms/research/projects/hmp/overview/ JCVI HMP] 50 genomes (oral,skin,vagina)
	* [http://img.jgi.doe.gov/cgi-bin/pub/main.cgi JGI IMG]		* [http://img.jgi.doe.gov/cgi-bin/pub/main.cgi JGI Integrated Microbial Genomes(IMG)]
			* [http://img.jgi.doe.gov/m/doc/about_index.html JGI Integrated Microbial Genomes for Metagenomics (IMG/M)]
	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=16729 HGMI at NIH]		* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=16729 HGMI at NIH]
	* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/16729_uncultured_bacteria/ HGMI TA] ~150K Sanger traces; trimming points are given		* [ftp://ftp.ncbi.nih.gov/pub/TraceDB/16729_uncultured_bacteria/ HGMI TA] ~150K Sanger traces; trimming points are given

Dpuiu: /* Online */

2008-06-09T15:51:44Z

Online

← Older revision		Revision as of 15:51, 9 June 2008
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	116771 43 3754 950 968 982 110875383		116771 43 3754 950 968 982 110875383
	* More than 50% of reads are from Proteobacteria; Gammaproteobacteria		* More than 50% of reads are from Proteobacteria; Gammaproteobacteria
	Proteobacteria ~~73261~~		Phylums:
	Firmicutes ~~15707~~
	Actinobacteria 10744		Proteobacteria 72634
	~~...~~		Firmicutes 15021
			Actinobacteria 10744
			Cyanobacteria 6877
			Chlorobi 4982
			Euryarchaeota 3266
			Chloroflexi 1277
			Bacteroidetes 1161
			Deinococcus-Thermus 809
			Total 116771
	* Organisms		* Organisms
	Burkholderia 12431 # Which one? B. cenocepacia AU 1054 , B. AMMD, B. sp. 383, B. xenovorans LB400, B. cenocepacia HI2424, B. vietnamiensis G4		Burkholderia 12431 # Which one? B. cenocepacia AU 1054 , B. AMMD, B. sp. 383, B. xenovorans LB400, B. cenocepacia HI2424, B. vietnamiensis G4

Dpuiu at 15:20, 9 June 2008

2008-06-09T15:20:26Z

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 * [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=16729 HGMI at NIH]
 * [ftp://ftp.ncbi.nih.gov/pub/TraceDB/16729_uncultured_bacteria/ HGMI TA] ~150K Sanger traces; trimming points are given
 * [http://en.wikipedia.org/wiki/Superfamily Wikipedia Taxonomic Ranks]
    domain
@@ Line 41: / Line 29: @@
    species:Pseudomonas aeruginosa group
    strain: Pseudomonas aeruginosa
 = HMP =

Dpuiu: /* Articles */

2008-06-09T15:11:42Z

Articles

← Older revision		Revision as of 15:11, 9 June 2008
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	* [http://nar.oxfordjournals.org/cgi/reprint/gkm846v1 IMG NAR 2007]		* [http://nar.oxfordjournals.org/cgi/reprint/gkm846v1 IMG NAR 2007]
	* [http://www.nature.com/nmeth/journal/v4/n1/pdf/nmeth976.pdf Accurate phylogenetic classification of variable-length DNA fragments., Nature Methods Jan 2007]		* [http://www.nature.com/nmeth/journal/v4/n1/pdf/nmeth976.pdf Accurate phylogenetic classification of variable-length DNA fragments., Nature Methods Jan 2007]
			* [http://en.wikipedia.org/wiki/Superfamily Wikipedia Taxonomic Ranks]
	[http://en.wikipedia.org/wiki/Superfamily Taxonomic Ranks]
	domain		domain
	phylum		phylum
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	species		species
	strain		strain
			* Example: Pseudomonas aeruginosa
	Example: Pseudomonas aeruginosa
	domain: Bacteria		domain: Bacteria
	phylum: Proteobacteria		phylum: Proteobacteria

Dpuiu: /* Lineage */

2008-06-09T15:11:16Z

Lineage

← Older revision		Revision as of 15:11, 9 June 2008
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	* [http://www.nature.com/nmeth/journal/v4/n1/pdf/nmeth976.pdf Accurate phylogenetic classification of variable-length DNA fragments., Nature Methods Jan 2007]		* [http://www.nature.com/nmeth/journal/v4/n1/pdf/nmeth976.pdf Accurate phylogenetic classification of variable-length DNA fragments., Nature Methods Jan 2007]

	~~= Lineage =~~		[http://en.wikipedia.org/wiki/Superfamily Taxonomic Ranks]
	domain		domain
	phylum		phylum

Dpuiu at 15:08, 9 June 2008

2008-06-09T15:08:54Z

@@ Line 23: / Line 23: @@
 * [http://nar.oxfordjournals.org/cgi/reprint/gkm846v1 IMG NAR 2007]
 * [http://www.nature.com/nmeth/journal/v4/n1/pdf/nmeth976.pdf Accurate phylogenetic classification of variable-length DNA fragments., Nature Methods Jan 2007]
 = HMP =

Dpuiu: /* Articles */

2008-06-09T14:23:01Z

Articles

← Older revision		Revision as of 14:23, 9 June 2008
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	* [http://www.nature.com/nrmicro/journal/v6/n6/pdf/nrmicro1901.pdf Nature Reviews: Microbiology in the post-genomic era]		* [http://www.nature.com/nrmicro/journal/v6/n6/pdf/nrmicro1901.pdf Nature Reviews: Microbiology in the post-genomic era]
	* [http://nar.oxfordjournals.org/cgi/reprint/gkm846v1 IMG NAR 2007]		* [http://nar.oxfordjournals.org/cgi/reprint/gkm846v1 IMG NAR 2007]
			* [http://www.nature.com/nmeth/journal/v4/n1/pdf/nmeth976.pdf Accurate phylogenetic classification of variable-length DNA fragments., Nature Methods Jan 2007]

	= HMP =		= HMP =

Dpuiu: /* Assemblies */

2008-06-06T18:51:10Z

Assemblies

← Older revision		Revision as of 18:51, 6 June 2008
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	* Longest ctg: ctg7180000029682 5252bp comes from NC_008499 35595 38.51 Lactobacillus brevis ATCC 367 plasmid 2		* Longest ctg: ctg7180000029682 5252bp comes from NC_008499 35595 38.51 Lactobacillus brevis ATCC 367 plasmid 2
	* Longest degen: ctg7180000030915 5920bp NC_008608 30722 56.32 Pelobacter propionicus DSM 2379 plasmid pPRO2		* Longest degen: ctg7180000030915 5920bp NC_008608 30722 56.32 Pelobacter propionicus DSM 2379 plasmid pPRO2

			minimus2 on AMOScmp & CA (ctg+degen) : most of CA assemblies were contained in AMOScmp contigs; stats about same as AMOScmp

Dpuiu: /* Assemblies */

2008-06-06T17:23:55Z

Assemblies

← Older revision		Revision as of 17:23, 6 June 2008
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	CA-scaff 4327 1000 48861 1682 1342 1456 7,278,044 76270 # OBT trimming of the reads		CA-scaff 4327 1000 48861 1682 1342 1456 7,278,044 76270 # OBT trimming of the reads
			CA-scf-unambiguous 4327 1000 26070 1473 1342 1403 6,374,650
	CA-ctg 4491 1000 5252 1419 1340 1388 6,374,863 # 4407 CONTAINED in references		CA-ctg 4491 1000 5252 1419 1340 1388 6,374,863 # 4407 CONTAINED in references
	CA-deg 11611 66 5920 850 833 898 9,865,902		CA-deg 11611 66 5920 850 833 898 9,865,902
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	CA:		CA:
	* Longest ctg: ctg7180000029682 5252bp comes from NC_008499 35595 38.51 Lactobacillus brevis ATCC 367 plasmid 2		* Longest scaff: scf7180000043951 48861bp(26070 unambiguous) comes from NC_007968 41221 38.26 Psychrobacter cryohalolentis K5 plasmid 1
	* Longest ~~scaff~~: ~~scf7180000043951 48861(26070 unambiguous)bp comes from NC_007968~~ ~~41221~~ 38.26 ~~Psychrobacter cryohalolentis K5~~ plasmid 1		* Longest ctg: ctg7180000029682 5252bp comes from NC_008499 35595 38.51 Lactobacillus brevis ATCC 367 plasmid 2
			* Longest degen: ctg7180000030915 5920bp NC_008608 30722 56.32 Pelobacter propionicus DSM 2379 plasmid pPRO2

Dpuiu: /* Online */

2008-06-06T17:03:15Z

Online

← Older revision		Revision as of 17:03, 6 June 2008
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	* 113 reference genomes : 89 complete, 24 incomplete		* 113 reference genomes : 89 complete, 24 incomplete

	#elem min max mean median n50 sum		#elem min max mean median n50 sum
	NC_ 173 3361 8264687 2184609 1966858 4317977 377,937,361 # come from 89 genomes & 70 plasmids ; some genomes contain multiple chromosomes		NC_chromosomes 103 943016 8264687 3569251 3481691 4326849 367,632,882
	NZ_ 3505 185 1802798 26389 9051 73891 92,494,763 # come from 24 genomes		NC_plasmids 70 3361 821788 147207 96488 300758 10,304,479
	~~total~~ 3678 185 8264687 127904 9940 3561584 470,432,124		NC_* 173 3361 8264687 2184609 1966858 4317977 377,937,361 # come from 89 genomes & 70 plasmids ; some genomes contain multiple chromosomes

			NZ_* 3505 185 1802798 26389 9051 73891 92,494,763 # come from 24 genomes

			N*_total 3678 185 8264687 127904 9940 3561584 470,432,124


	* 118084 Sanger reads from 3 insert libs (small,med,large)		* 118084 Sanger reads from 3 insert libs (small,med,large)